Justice League: Prime
by Azure Dragon of the East
Summary: When the World's Finest and Team Prime join forces to combat a global threat, The greatest force for justice is born. Supervillains and Decepticons beware. Follows a mix of both shows.
1. Secret Origins Part I

**Disclaimer: The following story holds characters and properties owned by DC Comics and Hasbro, Inc.**

* * *

 **Justice League: Prime**

 **Episode 1: Secret Origins**

Optimus Prime slowly trekked through the halls of the Omega One outpost, his spark seemed as heavy as ever. It had been a little over a week since the death of Skyquake and the day before that, Megatron who got caught in the Space Bridge explosion and one of their own Autobots: Cliffjumper. How he wished things could've been better between them all. If he was capable of shedding tears like humans could, he would have one for every Cybertronian life that had already been extinguished.

 _/Optimus, Agent Fowler is arriving soon/_ Ratchet's voice came over the comms.

"I will be there momentarily, Ratchet."

The Autobot leader turned around to return to the command hub; curious as to what could Fowler had come for this time.

* * *

The last Prime was greeted to the sight of Bumblebee and Arcee standing next to Ratchet while Bulkhead was with the children watching the television device humans seemed to be addicted to. He caught a brief glimpse of a human in a blue suit and red cape taking apart missiles. His attention was drawn to the sound of the lift doors opening and Agent Fowler walking out.

"Prime, we may have a situation. Over the past few months, a number of sites in the Deep Space Monitoring Network were totaled, the latest one being the radio telescope array in Texas a couple of days ago."

"Think the Cons are disabling them to bring an army?" Arcee asked.

"Unlikely. Their cloaking technology shields them from even our scanners, I don't see any reason they would need to," Ratchet countered, "Plus, with the complete destruction of their Space Bridge, it would take some time and resources before they can build another one and get it operational."

"Not only that, but nothing even hinting that the Cons were involved; no sightings. No evidence of large beings or vehicles going to or from the sites. No humans have claimed responsibility. Nothing." Fowler added as he gripped the guard rail and looked Optimus in the optics gravely. "This is making some of the top brass nervous, Prime; especially since the United Nations passed Senator Carter's Nuclear Disarmament Plan months ago. Superman's been going around disabling nukes left and right."

"Superman? Isn't he that human-looking alien who can fly in Metropolis?" Bulkhead asked.

Superman. From what Optimus recalled, the being by that name was also from a distant planet and raised by humans. His physiology allowed him to gain god-like power and yet he used his abilities in the defense and safety of humans. The last Prime had a measure of respect for the "Man of Steel" as he was sometimes called. While he applauded his courage at revealing himself to the world; Optimus held no illusions of doing the same with the Autobots any time soon.

"Among other things. Anyway, have you bots picked up anything odd recently?"

Optimus shook his head.

"Nothing out of the ordinary, Agent Fowler, but we'll notify you if anything does."

"I'll run a scan to see if-" Ratchet began but was cut off by the blaring sound of the alarm.

Ratchet rushed over to the console and activated the scanners. Bumblebee rushed over and beeped a question to the old medic.

"We have multiple unidentified objects approaching from deep space and they're approaching fast!" Ratchet reported.

"Decepticons?" Optimus asked.

"No Decepticon or Autobot signals detected; I don't think they're even Cybertronian. One just touched down in Metropolis! Another just hit Paris! Cairo! They're hitting everywhere!"

The bots looked at the map in shock as several dots peppered the map, indicating something had crashed at that site.

"Guys! Check this out!" Miko called over everyone, "A bunch of ugly things came out of the meteor in Metropolis. And they're tearing up the place!"

Fowler and the Autobots quickly gathered around. On the small screen, the saw three white tripod-like creatures laying waste to the city.

"What in Uncle Sam's beard is going on? Metropolis is Superman's turf, why isn't he ripping them apart?"

"He just upped and left; no one knows why," Raf explained.

"What are they? Have you ever seen anything like them?" Jack asked.

"Nothing that we've come across," Ratchet replied. "They appear to be organic in nature."

Their attention was ripped away from the TV by Optimus grunting in pain as he held his head.

"Optimus, are you alright?"

The last Prime snapped up, his expression was one of shock but then shifted into stern gaze.

"Ratchet, prepare to open the Ground Bridge."

"The Ground Bridge? What for?" The medic asked in confusion.

"I believe I know where we can get answers about this invasion."

Bumblebee, Arcee and Bulkhead then stood at attention near the Ground Bridge. Optimus gave Ratchet the coordinates while Fowler stood by the kids, if only to make sure Miko doesn't try to run off with them. With the coordinates locked and with a flick of a switch, the Ground Bridge's multicolored vortex came to life. Optimus joined his soldiers.

"Autobots! Roll out!"

With that, they all transformed and sped on into the Bridge.

* * *

Moments Earlier…

Superman was following Batman's plane after having just escaped the invaders at the military installation. Having picked up the mysterious J'onn J'onzz, they sought out some breathing room to get an idea of what was going on.

"That was close!" The dark knight said to his green passenger.

"We're not safe yet. Look."

Batman caught sight of a squadron of flyers heading right for them, they soon began to open fire on the heroes. Superman flew in to engage them while Batman ducked down into a canyon with several fighters on his tail. Weaving about in the confined area, the dark knight managed to take out a few with the narrow walls before one literally clipped his wing; sending him and J'onn spiraling down. Things certainly looked bleak until…

"What happened?" Batman asked as the plane was encompassed in a green glow.

"Help has arrived." J´onn said calmly.

Batman looked through the window of the canopy and, standing upon a cliff side, saw that John Stewart; assigned Green Lantern of sector 2814 had arrived. The former Marine kept a firm grip on the damaged plane as more fighters attacked. Another ally came in the form of a woman with a hawk face mask, and wings on her back, wearing green pants and yellow shirt that left her shoulders free. She wielded a mace covered in electricity, giving a war cry as she beat the fighters to death.

"Hawkgirl? What is she doing here?" Batman asked.

J'onn said nothing as he phased out of the plane and joined Lantern and Superman.

"Sorry I'm late, there was an uprising on Rigel 9." John Stewart said as he placed the plane down and charged at the incoming fighters with Superman, J'onn and Hawkgirl. The Man of Steel plowed through a number of fighters, chucking away one of them into the mountain side. Green Lantern used his power ring to slice up a few of them. J'onn engaged the fighters using his intangibility to trick them into destroying one another. Hawkgirl managed to dodge many blast but one strayed in front of her and loosed shrapnel at her, with a cry she fell and was in long for a death blow, fate intervened then as a woman like no other appeared. The woman was tall, with raven hair and quite beautiful to the eye, wearing red boots, golden belt, a one piece suit of red, yellow, blue and white stars, a golden lasso was on her waist, and a golden tiara on her head with a red star.

"Allow me." She said before she deflected every shot fired with her bracers back at the ship.

The redirected fire damaged the fighter enough to send it careening out of control, right at Hawkgirl and the mystery woman. Acting quickly, Green Lantern formed a shield around the two just before the disabled ship crashed into it; leaving the two women unharmed.

"Who's the rookie in the tiara?" Stewart asked.

"I´m not sure," Superman replied as he hefted a fighter and threw it towards a canyon wall.

On the bottom floor a red streak could be seen heading towards the Dark Knight, carrying the wing of his damaged plane.

"Hey bats, I think you dropped this." Said a man in a crimson red body suit, the Flash had arrived.

"More fighters coming in!" J'onn cried out.

Twelve more fighters were approaching fast and ready for another fight with the heroes. Not a moment later, however, a swirling vortex of energy erupted nearby.

"Now what?" Batman asked.

He got his answer when a green truck came barreling out of the vortex at high speed and jumped the cliff right at the incoming fighters. To everyone's shock, the truck's body shifted and rearranged itself until it resembled a giant metal humanoid; its right fist then changed into a mace-like weapon. Bulkhead, using his momentum and mass, smashed into the first fighter; breaking it in two, then broke off the wing of the next one before grabbing onto a third and climbing onto its top.

"Knock, knock," Bulkhead quipped as he brought his mace down hard.

A yellow muscle car and a driverless blue motorcycle came out next and they two changed into robots before jumping onto the fighters, their hands now transformed into blasters as they fired point blank into the ships they were on. The ships began to plummet to the ground and towards each other; prompting Bumblebee and Arcee to bail as the ships crashed into each other. This drew the attention of half of the remaining fighters to them; the two Autobots responded by returning fire. A few shoots easily took out the four ships. The three remaining ones closed in on Batman and Flash.

Finally, before the vortex closed, a red and blue semi-truck roared out and transformed as well; leaping in front of the two human heroes. His right hand changed into a blade as the first fighter open-fired on them. The ship got too close as Optimus drove his blade into the invader craft who then used it as a shield from the other two. When they passed over, Prime threw his make shift shield at them; only hitting one of them before he drew his Ion Blaster scored a direct hit on the other. He turned his attention to the human heroes; his face guard retracted.

"Are either of you injured?" he asked them.

"Uhhh…no, w-we're good," Flash answered as the other heroes landed beside them, handing Batman the broken plane wing.

The other three Autobots approached slowly.

"Good thing they break easily," Bulkhead joked with his teammates.

"I think we've had more trouble with Vehicon troopers," Arcee said smugly, Bumblebee chirped in agreement.

"Okay, this day just went to a whole new level of weird," Flash grimaced before he caught sight of the mystery woman out of the corner of his eye.

"Whoa! Where have you been all my life?" The Flash asked.

"Themyscira." She replied innocently.

"Huh?"

"The Home of the Amazons? I thought that was just a legend," Hawkgirl said as she and the others gathered around.

"I assure you, it's as real as the ground on which we stand. I am Diana, princess of the Amazons." The raven haired spoke in all seriousness.

"Pinch me, I must be dreaming," Flash exclaimed, not sure how to process what's been happening. Superman elbowed him in the arm.

"Themyscira is protected by the gods, but I could not stand idly by as the rest of the world was in danger." Diana continued.

"It was lucky you showed up when you did." Superman spoke but J´onn intervened.

"No, not luck I telepathically summoned her just as I did them," he said looking at the Autobots.

"And just who are you guys?" Green Lantern asked.

"We are autonomous robotic organisms from the planet Cybertron; or Autobots for short. I am their leader, Optimus Prime," Prime explained.

"Cybertron, I don't think I've heard of that planet before," Stewart responded.

"Look I'm usually pretty quick on the uptake but can someone please tell me what the heck is going on here?" Flash asked what many almost forgot about.

The Martian paused to prepare them for his tragic tale.

"I believe it would be best if we continued this discussion in a more secure location. The enemy is likely to send more troops when the ones we just engaged do not report in; if they haven't already," Optimus said.

"The big guy has a point; we're sitting ducks out here," Green Lantern agreed.

"I suppose you know a good spot," Flash asked Optimus, who placed a metal finger to his comm.

"Ratchet, open the Ground Bridge; we're returning to base. And inform Agent Fowler that we are bringing some guests."

 _/Roger that, Optimus/_

Another vortex opened up in front of the heroes.

"This Ground Bridge portal will take us to our base; we can all be briefed on the full situation there. Agent Fowler, our liaison to your government would no doubt like to hear this as well."

Reluctantly, the heroes slowly entered the Bridge followed by the Autobots; the portal closing just as more fighters arrived.

* * *

After the human heroes got over the nausea, they took in their new surroundings.

"Whoa, what is this place?" Flash asked.

"Looks like an old Cold War-era bunker," Stewart guessed.

"Welcome to Autobot Outpost Omega One," a man's voice called out from the catwalk. "I'm Special Agent William Fowler. Prime, mind telling me why you brought these guys here?"

"I had them brought here because one among them is willing to share what he knows of the invaders and we could use all the help we can get."

"Where's Jack, Miko and Raf?" Bulkhead asked.

"I had them sent home; safest place for them to be right now. The invaders are targeting the major cities first so I'd say Jasper, Nevada is safe for the time being," Fowler answered, "Now then, what exactly are we dealing with?"

Everyone turned to J'onn as he grimaced; steeling himself as he told his sad tale.

1000 human years Mars was habitable, they were peaceful and advanced, but then they came. It was unknown where they originated from, but their intentions clear as they wanted the lush world for themselves. Though pacifists, the Martians soon learned how to wage war in an effort to drive of the invaders, but centuries of warfare decimated the planet, his people hunted and either captured to be fed upon for their physic energies like parasites or killed.

They stole their shape shifting abilities, erased their civilization, until finally a handful of survivors launched a desperate attack. They fought their way into the heart of their citadel, until J´onn was able to release a powerful nerve agent that left them in a catatonic state. The price paid for this victory however was J´onn became the last of his people. So he took it upon himself to guard the creatures, but when astronauts came and released them during his hibernation period; with nothing to stop them, they planned to add Earth to their list. Barely escaping, he came to deliver a warning only to be captured.

"Wait, those astronauts never said anything about finding life on Mars." Flash spoke.

"Hmph! Some pencil pusher in Washington must have decided it should be classified information." Stewart added.

"I don't believe that is the case," Optimus interjected.

"What do you mean?" Batman asked wondering what he saw that no one else did.

"J'onn, you said that these invaders stole your race's shape shifting abilities, correct?"

"Yes"

"Then it may be possible that those astronauts never returned from Mars but rather imposters did. Agent Fowler, do you know who was on that mission?"

"Yeah, Ed Reiss and-" Fowler stopped in realization, "-and J. Allen Carter, the senator who pushed for the Nuclear Disarmament Plan. The phony got into a place of power so he could take out our heavy artillery."

"And explains why they sabotaged the Deep Space Monitoring Network; so we couldn't track their activities," Batman added.

"We got to stop them before it's too late." Lantern said as he raised his fist in defiance and his eyes glowed with power.

"It may already be too late." The last Martian said in an ominous tone.

"Optimus, I think you should see this," Ratchet called over.

All eyes turned to the monitor where a news broadcast from Metropolis was broadcasting from the impact site. Suddenly, the meteor broke apart and from the crater, massive tendrils suddenly broke out and reshaped themselves in to strange shaped objects. From a hole in the bottom, a drill bore and pounded into the Earth and in a scene similar to a morbid heartbeat, smoke and debris were expelled into the atmosphere.

The heroes watched as a cloud rose and covered the sky.

"What is that?" Diana spoke in alarm.

"It´s begun." J´onn said in finality.

"What are they doing?" Hawkgirl asked as she looked to the green man for answers.

"The invaders are nocturnal; they want to blot out the sun to live in perpetual darkness." He said in a grim tone

"Friends of yours?" The fastest man asked in humor at the Bat.

"This is no joke." He snapped back.

"What´s the big problem can´t you just whip up some more of that nerve gas." Flash said as he moved to the Martian's side.

"Unfortunately no, the gas can only be made from a rare Martian plant, I brought a sample with me but it was destroyed when I was captured" answered the green alien with the same monotone voice.

"Uh, what´s plan B?" The young hero asked lamely.

"Can't call in air strikes, everyone is preoccupied by all the walkers and if Carter was a spy, there's no telling who else could be. Without knowing who to trust, we're on our own," Fowler said.

"We'll have to take out those factories." Diana broke the silence.

"Agreed, surgical strikes may be our best course of action. If we divide into teams and Ground Bridge to sites where security is minimal, we might be able to gather more intel and disable those machines," Optimus added.

"Now hold on, this is no job for amateurs or metal giants we know nothing about. How do we know we can even trust you?" Lantern voiced his displeasure.

"Hey, Glow stick! Prime and his team saved my star-spangled shorts and this planet while you've been flying around in your PJs. They've earned my trust and you can quote me on that," Fowler raged at Stewart.

"Let's not fight amongst ourselves," Superman tried to play peace maker.

"I assure you all, we'll explain everything once the crisis has been averted," Optimus attempted to placate everyone as well.

"Right, first things first. So who's go with who?" Fowler asked them all.

"Dibs on the Amazon." Flash moved fast next to the princess who gave a wide eyed impression.

Everyone else stared at the speedster.

"What?"

* * *

 **A/N: Yeah, I know; a new story but I wanted to see how this concept would work.**


	2. Secret Origins Part II

**Disclaimer: The following story holds characters and properties owned by DC Comics and Hasbro, Inc.**

* * *

 **Justice League: Prime**

 **Episode 2: Secret Origins Part II**

Bulkhead and Bumblebee raced at high speed towards the invader structure in the South American region, Flash and Green Lantern in their respective driver seats; the scarlet speedster enjoying the slick muscle car.

"I gotta get me a ride like this," He said grinning.

"Let's focus on the task at hand, Speedy," Green Lantern said through Bumblebee's comm.

"You are no fun," he said to the man.

"This isn't supposed to be fun, we have a job to do and we will do it better without any distractions, understood?" He replied gruffly.

"Yeah, yeah, I hear ya."

"You two always like this?" Bulkhead asked.

"This is our first work together," Flash replied, "So, Bulkhead was it? What kinda place is this Cybertron?"

"When it was in one piece, beautiful."

"Why, what happened?" Lantern joined in.

"War"

Flash grimaced, thinking it wise to change the subject.

"Uh… How come that other bot didn't go on these missions?"

"You mean Ratchet? He's our medic and prefers to stay behind. Besides, he wanted to study some of that goo he found on me."

"What for?" Lantern asked.

"My guess, find a weak spot on this blobs."

Within an hour, they arrived at the jungles that surrounded the complex; three Walkers moving around the perimeter. Bulkhead and Bumblebee had transformed, using the trees as cover, while Flash and Stewart ducked behind some upturned stones. The four observed the situation and began to formulate a strategy.

"That´s our target, now listen up here´s the plan…"

"What plan? We kick their butts right? Let´s get this over with." The crimson clad hero said before he ran down, leaving a disgruntled Lantern.

"This isn't gonna end well," Bulkhead stated.

Flash moved near the alien guardian and gave a whistle to get its attention…it worked as it locked on and fired.

"Hah! Missed me!" he mocked as the blast hit 4 feet to his right thanks to his speed, not waiting for another shot, he ran beneath them as they tried to eliminate him.

However he did not see the trap in front of him until…"BANG!" He soon found himself incased in a thick sticky slime that kept him in place, one of the Walkers came to capitalize on his predicament. The Walker didn't get the chance to carry out its intent due to a well-placed shot of energon to the bio-machine's "eye." A hail of laser fire, courtesy of Bulkhead and Bumblebee, began to push it back but also caught the attention of the other two Walkers.

"We'll cover you, go!" Bulkhead called out.

"Hang tight, hotshot!" the Lantern spoke before he flew towards him.

"Heh…I'm sorta stuck here." Flash said weakly to his ally.

"I hope the others are having better luck than we are." Stewart said.

* * *

In Egypt…

Group 2 Ground bridged a mile away from the complex. From there, their Martian ally scouted ahead, while Diana flew and Batman rode on Arcee to the factory; using the terrain as cover until they reached the nearby ruins. The Autobot remained in vehicle mode as Batman peered at the facility as a Walker passed by.

"Hiding like cowards is not the Amazon way," Diana spoke.

"Take it easy. First, we find a weak point in their defenses. And when we find it, we hit 'em hard." Arcee replied, trying to placate the Amazon.

J'onn came back at that moment.

"I have scouted the outer walls, there are no openings."

"Then we'll make our own!" Diana declared before flying after the Walker. J'onn made an attempt to stop her but Batman stepped in.

"Wait…let's see what she can do." He said.

She shot towards the Walker while pulling her golden lasso free, dodging fire in the process. Like a cowboy in the old west, she swung it around and grabbed the leg, and then much to the shock of the men looped the rope around the legs, finally stopping on one of the legs.

"Hera give me strength!" she said before giving a mighty pull, the force so great the legs closed in, the result was the Walker losing its balance and landing on the wall, crushing it completely.

"There's your opening." She said as she stood over the remains.

J'onn went in, while Batman voiced a simple "not bad" as he hopped onto Arcee and rode up to the opening.

The two followed the Martian and were assaulted by a group of aliens. Arcee quickly transformed and returned fire while Diana blocked their shots, forcing the invaders to make a hasty retreat, however one did something rather…odd. This one seemed to run but then skip to the right as if to avoid something.

"They run like cowards! What are you waiting for?" Diana exclaimed as she gave chase followed by J'onn and Arcee. Batman, however, hanged back. He saw that alien's strange behavior and then turned to look at opening.

* * *

In Metropolis…

Team 3, composing of Hawkgirl, Optimus Prime and Superman, got into the thick of things as soon as they arrived as they took on the alien assault. The Thanagarian quickly showed her warrior nature as she pummeled a Walker into the ground with her mace giving a war cry every time she struck. Optimus drove his blade through another before cleaving it in two then fired upon a few invader troops after being pelted in the back. Superman then appeared on the machine downed by Hawkgirl and gave a swift chop to the leg, grabbed it and then used it to force entry into the complex.

"Hawkgirl! Optimus! Follow me!" he yelled back at them as he went inside, the two soon followed.

They entered into complex, the insides a mass of curves and tunnels yet spacious enough for Optimus to walk around.

"Keep a sharp eye out." The Prime told his two companions as he scanned the area, his ion blaster at the ready.

"I always do."

Soon however they encountered resistance from the invaders.

"Stay back, I'll-" Superman never got to finish.

With a war cry, she threw herself into battle swinging and smashing them for all her worth, one went into the direction of the last son who ducked, letting the alien hit the wall with a resounding splat.

"Whoa" the man of steel said as he stared in her direction.

It ended with the remains of the aliens decorating the walls.

"What? There's a time for words and a time for action." She said casually as she neared him surrounded by the unconscious creatures, the other two simply looked on.

* * *

Back with Team 1

Lantern was cutting the Flash free of the slime while the two Autobots stood in front to protect them; firing at the numerous Walkers that had joined the battle.

"Of all the idiotic, boneheaded, glory-grabbing moves! Haven't you ever heard of teamwork?!" Lantern fumed at the speedster.

"Uh maybe you should the motivational speeches till later!" Flash quipped after a laser bolt hit a few feet away from them.

The slime had been weakened enough for Flash to finally free himself. Lantern flew upward and placed a shield around himself. It deflected several blast, however the aliens then fired a strange pod that released a yellow gas that clearly did not agree with him. Bumblebee attempted to grab him but got hit in the side, knocking him down. Thankfully the speedster quickly spun his arms at such a speed he blew the gas away from the knocked out Lantern.

"GL!" he spoke only to look up to more and more Walkers closing in.

"It's not good! We gotta retreat!" Bulkhead called out as he got clipped in the shoulder.

"Uh oh, got to run." He quipped before picking him up and running for safety, the two Autobots following close behind in vehicle mode.

* * *

Back with Team 3

The trio made their through the factory and, strangely enough, had not encountered any resistance. And in Optimus' experience, that's usually not a good thing.

"It's far too quiet," Optimus voiced his concerns as they all came to an opening.

"They´re close by, I can almost smell them." Hawkgirl said in a dangerous tone.

"Are you always so eager to fight?" Superman asked.

"My home, Thanagar, is a war like world. There, one must strike first or die." She replied.

Neither the man of steel nor the last prime got a chance to retort as laser blast flew right past the latter's face. They turned to the right and saw three creatures run through a sealing door. Superman looked back to find the door they use seal itself as well. Soon vents opened up and Hawkgirl was hit by the same knock out gas GL suffered from.

"Hang on Hawkgirl I´ll…AAARRRG!" he screamed as thousands of volts of electricity hit him and Optimus. Prime hammered on the door with all his might but succumbed to darkness.

* * *

With Team 2

The sounds of laser fire filled the air as the aliens once more cut off the group. Diana shielded herself and her comrade with her bracers while Arcee bought her some breathing room as she fired her blasters at the invaders, their bodies reacted rather harshly to the blast as the energon practically fried them.

"They have cut us off again!" Arcee groused after hitting one in the leg.

"It's like they know where we are heading," Batman added before firing an explosive batarang that caused them to flee.

They all turned to J'onn for answers when they saw his eyes glowed then stopped.

"Superman's team is down, they have failed." He spoke his tone seems to drop a bit indicating his remorse at the situation.

"What! Are you certain?" Diana asked in disbelief.

"I can sense it," He nodded, making her heart drop at that.

"Do they live?" the Autobot asked as she took cover behind a pillar.

"Yes, they have been taken prisoner, most likely for interrogation…or feeding." His voice clearly telling them his disgust at the idea. "This way, hurry!" He pointed to an opening.

Through the maze-like complex they went; dodging and firing on invaders along the way, until finally they had arrived at their destination. The aliens were working diligently; unaware of the heroes' arrival.

"It's the central core," J'onn explained.

"How do we shut them down?" Batman asked as gave the scene a look and clearly did not like it.

"I am going to take a wild guess and say that's important." Arcee suggested spoke as she pointed to what appeared to be some sort of crystal in cased in a force field.

"Yes, the ion matrix crystal. If we can remove that, it will shut down the whole plant. I will need a diversion." He said to them.

"You got it," Batman spoke as he threw another batarang to sever a stem conduit, spilling black liquid on nearby invaders.

Diana doing the same by pulling out a nearby tube. Arcee dropped down and transformed then preceded to ram and swipe the aliens; all to draw their attention away from the Martian as he phased through the floor towards the crystal. He succeeded in its capture but one guard who had not been drawn in by the three, fired upon him in hit his back. Soon more soldiers' came to engage the three.

"Get J'onn out of there, we'll cover you!" Batman ordered as he took out an electrified silver knuckle and beat back the aliens with a good shock to their systems. Diana quickly grabbed the Martian in the frenzy and went for the exit as Arcee continued to clip the invaders in motorcycle mode. She came to a stop in front of Batman, allowing him it to climb on and follow their comrades; picking up the crystal along the way. Diana and J'onn quickly made through the exit, but it sealed before Arcee and Batman could make it out. Batman beat at the door, causing the electricity to spark but nothing more and Arcee slashed at it with her elbow blades; however the cuts sealed faster than she could damage it. Both turned around to a horde of aliens pointing their weapons at them.

"Do you think if I surrender the crystal they'll let us live?" Batman asked as he considered all possible escape routes.

"Not likely," Arcee replied.

The dark knight in response simply dropped the crystal.

"Batman! Arcee!" Wonder Woman yelled as she prepared to rip the door off when the sounds of laser fire came, followed by small impressions on its shape.

"No!" she yells now even more determined to charge the door.

"Wait! There's nothing more that can be done for them." He said to her solemnly.

"You mean they're…" she began.

"…gone" he finished.

"Hera help us." She prayed, before they left the place to regroup with Lantern, Bulkhead, Bumblebee and Flash.

* * *

Mere seconds earlier…

The weapons of the invaders gave off a low hum of power, indicating they were about to fire. Suddenly, the familiar energy vortex of the Ground Bridge opened right next to them. Arcee quickly grabbed Batman and dove for the portal, dodging the laser fire by centimeters; the portal quickly closing with the two inside.

* * *

The two exited out of the Ground Bridge at the Autobot base.

"Welcome back" Fowler said to the dark knight.

"Thanks for the save, Ratchet," Arcee sighed relief.

"It wasn't easy. Their machines are starting to cause interference on the comms; I barely understood you calling," he said as he shut down the bridge. "I hope you have some good news."

"The attack failed and we had to leave the vital component to their factory behind," Batman replied with a scowl.

"Bulkhead and Bumblebee's team didn't fair so good either. They were here a few moments ago; I had bridged them to outside of Metropolis to regroup with the others but I soon lost contact with them. I still haven't been able to reach Optimus' team."

"J'onn told us that they've been captured," Arcee said grimly.

Ratchet opened his scanners.

"I'm still picking up his life signal; meaning they're still alive. I'll bridge you to Metropolis to join the others," Ratchet went for the Ground Bridge controls.

"No, wait!" Batman shouted, causing Ratchet to halt. "This may be an opportunity. J'onn is currently shielding us from being detected by the invaders; they think we're dead."

"I see. That _would_ give us a tactical advantage for the moment. Perhaps even figure a way to disable their factories," Ratchet said as he rubbed his face plate.

"I noticed that they seemed to avoid sunlight, almost as if they're afraid of it."

"I'd say they're more than afraid of it." Ratchet turned their attention to the screen, "I've been running tests on some of that sludge I got off of Bulkhead and it seems to breakdown and collapse on the molecular level when exposed to ultraviolet light. This type of condition normally manifests in species that reside in deep space away from any nearby stars."

"So they can't handle sunlight?" Batman deduced. "That won't do us much good since they're blocking out the skies."

"You said something earlier about a vital component to their factories; what was it?"

"J'onn told me that the factories all have an ion matrix crystal at their heart."

"An ion matrix crystal? If that's what those things run on then we might be able turn their own machines against them," Ratchet scoffed as he went to the table and started to look for something.

"Let me guess, reversing the ion charge?" Batman asked.

"Exactly. Using ion matrix crystals is rather tricky since if the charge is reversed, whatever it was plugged into will do the opposite of what it was intended for," Ratchet then held up a small device in his large metal fingers; "This should do it."

The medic handed Batman the device, "Attach that to the crystal and the factory will do the rest."

"Alright, we got plan and an opening. Let's roll," Arcee said to Batman.

"Not so fast, I'm coming with you. You'll need all the help you can get," Ratchet declared.

"I'll stay and monitor the situation from here. That way, I can bridge you out before anyone sees you," Fowler added.

"Thank you for that, Agent Fowler. But Optimus had figured that by getting involved with this invasion meant that we'd have to reveal ourselves to the humans. And after everything that's happened up to this point, I'm willing to bet that humanity is already fully aware of our existence now. All we can do is finish the mission."

Fowler remained silent as he stared at the Autobot medic then activated the Ground Bridge. He remained so as he watched Ratchet, Arcee and Batman walk into the vortex, ready for the battle to come. He couldn't help but agree with Ratchet's belief of humanity now knowing about the Transformers. He hoped that they would see that the Autobots were on their side. He hoped that they would stand with them against the Decepticons. He hoped…. They would accept them.


	3. Secret Origins Part III

**Disclaimer: The following story holds characters and properties owned by DC Comics and Hasbro, Inc.**

* * *

 **Justice League: Prime**

 **Episode 3: Secret Origins Part III**

J'onn and Wonder Woman waited for Flash and Green Lantern's group while looking at the chaos cause by panic and the fear of people, the authorities hard pressed to maintain order.

"Perhaps mother was right about mankind. They're nothing but untamed savages." Said the princess looking the chaos with sad eyes.

"Do not judge too harshly, they act out of fear." Said the blue skinned alien in monotone tone as they watched on.

Down below, a pair of bikers were attempting to move a large slab of concrete.

"Hey, there's kids trapped under here; someone give us a hand!"

As if on cue, a familiar green truck and yellow muscle car passed by before Bumblebee turned around and approached the two. He then transformed in front of them, much to their shock; and pulled the concrete away enough for the two men to pull the kids out. After receiving a stunned thank you from one of the bikers, Bumblebee transformed and drove off to meet up with J'onn and Diana. Green Lantern and Flash soon joined them after making sure the civilians were safe from the looters and criminals.

"Sorry for the delay, we had to help some civilians." The former marine said.

"So what did you call us back for?" The Flash asked.

"Superman, Optimus and Hawkgirl have been taken captive, they're somewhere inside that facility," J'onn said as he pointed at it, darkness and lighting adding to its already macabre feel.

Flash resisted the urged to shiver at the sight.

"Where are Batman and Arcee?" GL asked as he saw they were not with them.

"They acted heroically…to the very end," J'onn replied grimly.

"You mean they're gone?" Flash asked in disbelief.

Bulkhead and Bumblebee were taken aback but then grimaced in sorrow. Stewart saw this; thinking that these guys have heard similar words far too many times.

"This is not good, definitely not good," he said as he looked at the facility.

"We gotta go in there and get them out!" Bulkhead declared as he slammed his metal fist into his palm

"If they're still in there, we _will_ go in and rescue them," Lantern assured the green Autobot.

"We will have to hurry, though. The Imperium is coming," J'onn added.

"The who?"

"The supreme intelligence that controls these invaders; we have met before," J'onn explained with a bit of anger in his voice.

"Alright, we're going in. Here's the plan…"

Stewart's plan involved Flash acting as a diversion for the remaining walker while the others stormed the facility. What guards they had were dispatched easily on the outside and in. As they moved further in, J'onn couldn't shake the feeling that something was off. Recalling the times he and his fellow Martians stormed the bases of their enemies; J'onn couldn't remember a moment when security was this lax. Soon, they found the holding cells that contained Superman and Hawkgirl; their arms and legs incased in a hard substances heads down as if they were asleep. Flash, Stewart and Diana rushed over to free their comrades as Bulkhead and Bumblebee stepped inside; the former asked the one thing they failed to notice.

"Wait, where's Optimus?"

That's when J'onn felt it.

"It's a trap!" He yelled, but it was too late as they suddenly awoke and morphed into their true forms, the chamber was sealed and the gas they used before knock the human heroes all out. Electricity ran through the cell, shocking the two Autobots until they too passed out.

* * *

J'onn was brought back to the waking world by the sound of someone calling his name. When everything came into focus, he turned to find Superman and the others had been, for lack of a better term, "glued" to a slab to keep them in place. Even the titanic Autobots had been trapped in such a manner though it seems that extra was applied for good measure.

"You shouldn't have risked your lives for us," the man of steel lamented.

"Would you have done less for me," J'onn replied.

Before more words could be exchanged, a single invader stepped forward.

"Earth's mightiest heroes, welcome."

It then shifted into a more familiar form: Senator J. Allen Carter.

"So it was you," Superman stated, surprising the fake that they had figured out his involvement.

"Unfortunately, the real Carter never returned from Mars," the phony gloated.

"And you used your new position and Superman to weaken Earth's defenses," Optimus added.

"He was so eager to cooperate. Thanks to his efforts, the humans were completely helpless against us."

"It's not over yet," Superman growled defiantly.

"Wrong again, Superman"

* * *

Outside, Batman and the two remaining Autobots observed the facility that held the rest of the captives.

"Security seems lax on the outside," Ratchet noted.

"They must be inside, the others are no doubt being guarded. They must be expecting something," Batman added his observations.

"Look up there!" Arcee suddenly spoke as a massive vessel pierced the heavens.

"This must be the leader of the aliens." Ratchet said while Batman nodded.

"We are running out of time, I have to get this emitter inside to reverse the ion flow," The Dark Knight said to the Autobots.

"Alright, we'll help the others but once the fighting starts things will get intense," Ratchet said in return and Batman nodded as they both went ahead towards the complex.

As they made their way into the core, a smaller vessel had detached itself and landed in fronted of the captured heroes. The three watched as a hideous creature emerge from it. Soon enough, the fake Senator Carter along with the other invaders bowed to the Imperium, leader of the aliens. J'onn was deposited before the Imperium; it then struck him, reverting J'onn back to his natural form. Soon screams were heard as they saw how the leader mocked and tortured J'onn, burying its tentacles into his body, both having to resist the urge to help him as they made their way to the main chamber where the crystal was held.

"Optimus, this is Ratchet. If you can hear me, stand by; we're here to rescue you all," the medic whispered into his comm; the Prime nor the other Autobots made any sign of acknowledgment so Ratchet could only pray that they heard him.

Once there, Batman tried to cut through with a miniature laser but it proved too time consuming. The dark knight removed something from his belt and sprayed some kind of foam over the casing. He silently signaled the bots that he was all set on his end as Ratchet handed Arcee a flashbang grenade.

"Get ready," Ratchet said; J'onn sensed this and made it known that now was the time.

"NOW!"

Batman hit the detonator, blowing a hole in the casing. He then got to work by inserting the emitter and activating it, the red veins suddenly turning blue.

"Guys!" Flash yelled in shock and awe.

"It can't be!" Wonder Woman said in shock.

"I mentally shielded them from detection." The Martian spoke as regained his chosen form and strength.

"What have you done!" the Carter doppelganger yelled.

"Reversed the ion flow," Batman said casually.

"DESTROY THE CRYSTAL!" The alien leader ordered; a number of soldiers fired at the containment field only for the shots to bounce of harmlessly.

"It's shielded!" The fake Carter exclaimed.

Soon the tables turned even more for the heroes as the sun broke through the clouds and bathe all in its light, the aliens melting and scurrying like rats in a doomed vessel.

The Imperium flesh was bursting as he tried to hide in the shadows, but J'onn had something to say about that.

"You live underground and shun the light! Why! Does it burn your pale, putrid flesh!" He yelled at the creature he held in place, taking some measure of joy at hearing the cries of the destroyer of his people.

Some of the invaders drew their weapons, ready to fire at the last Martian. Arcee threw the stun grenade, drawing all their attention. The sudden flash disoriented the invaders long enough for Ratchet to hop down, flipping out his blow torch and began to work on freeing the others; starting with Optimus. Batman followed suit and began working to free Diana.

"What's up with them?" Bulkhead asked; watching a few invaders practically melting in the sunlight.

"Ultraviolet rays; coming from deep space, the invaders have no resistance to our sun's radiation," Batman explained.

The sun had a far different effect on Superman. After a much needed recharge of solar energy, the man of steel cut the resin holding his arm and place; freeing himself.

"So you did find a weakness, after all," Diana spoke as she was finally freed.

"KILL THEM ALL!" the Imperium screamed; those still capable of fighting complied.

Just as the invader leader said this, Optimus had managed to wrench one of his arms free and draw his ion blaster. He fired off a few shots to disperse the invaders about to fire long enough for him to turn his sights to his other trapped limbs and blast it free from the resin. Arcee joined the group as she primed her blasters and provided cover fire. The now freed Superman shielded the others by ripping off a piece of the platform and bent it to cover them. In that time, Ratchet had just managed free up Bulkhead's arm, allowing him to bring out his own blaster and shot one of Bumblebee's arms loose. Superman turned back and used his heat vision to cut Hawkgirl's restraints; particularly, the hand holding the mace. The Thanagarian used said mace to break free Green Lantern's ring hand just as Diana broke Flash's feet free.

The others soon joined the battle; Hawkgirl bashing aliens left and right with her mace, Bulkhead using his own mace fist to smash invaders and structures they stand on, Flash using his speed punched all in his path, Stewart with the help of his ring blasted them from up high, Superman decided to make some more windows and punched holes in the ceiling, one of these hit Carter full blast and melted him into a puddle. Bumblebee, Arcee and Optimus fired at the walls, allowing more light in, making it difficult for the invaders to move around with melting. Ratchet drew his blades and cut a rather large gash in the wall before he and Diana ripped it wide open.

The Imperium freed itself from the Martian and entered his shuttle. As it began to ascend, Diana caught sight of it and used her lasso to rope the tail and keep it in place; that is until a laser was fired from it forcing her to shield herself and let go. It seemed the leader would escape until a big metal fist gripped the lasso. The fist, belonging to Bulkhead, pulled with all his might while he tried to keep himself in place but it was proving to be a struggle as the ship increased its speed to escape. Diana returned and grasped her lasso and began to pull alongside the green Autobot. While they kept the ship in place, Hawkgirl flew up to the front of the craft.

"HUAAHH!" she screamed as she bashed her fully powered mace into the hull. She did this multiple times until finally it was too damaged to move; allowing Bulkhead and Diana to pull the ship back down and crash into the facility, killing the leader of the invaders.

The crash weakened the structure, causing a chain reaction and now the heroes needed to get all the prisoners out. Once the complex fell, and all turned to the sky to see the creatures make an escape.

 _/Prime, it's Fowler. You guys okay?/_

"We are fine, Agent Fowler. The facility in Metropolis has been destroyed, along with the leader of the invaders," Optimus said into his comm; drawing everyone's attention.

 _/Where there any civilians inside?/_

"Yes, but they have been rescued and are awaiting medical attention."

 _/Understood. Looks like a retreat has been sounded; they're all pulling back into space. However, there's still some squads left behind./_

"Understood, prepare to open the Ground Bridge."

"Everything okay, big guy?" Flash asked.

"With the loss of their leader, the invaders are retreating but there are still some pockets of resistance. Agent Fowler is about to open the Ground Bridge to base; we can plan from there."

"What about you telling us your story?" Lantern added.

"We will tell you, you have my word," Prime assured Stewart just as the Ground Bridge opened.

Once there, clean up began. Facilities were demolished, the remaining invaders were either destroyed or fled to the depths of space, and through it all the heroes did so together. The media caught wind of it and documented their efforts, As Ratchet surmised, the Autobots were caught on camera and now the world was fully aware of their existence. Finally, when all was said and done, the world breathed a sigh of relief but there were still a few questions on their minds: who are these metal titans? Will the invaders return? What happens now?

* * *

The Autobots and heroes filed out of the Ground Bridge. The Bots gathered to one side of the room while the heroes of Earth did so on the other. Optimus then spoke.

"As agreed, I shall explain who we are. We are Autobots from the planet Cybertron. "

"So why are you here?" Lantern asked.

"To protect your planet from the Decepticons."

"Okay, what are Decepticons and why are they here?" Flash asked growing more confused.

Optimus then went into detail of the Cybertron civil war, mostly over control over the planet's supply of Energon; the fuel and lifeblood of their race. He then went to describe the leader of the Deceptions and Optimus' former brother-in-arms, Megatron. When their planet had been rendered uninhabitable, the Autobots had to leave and find a new world. However, the Cons attacked en-route and both sides ended up crash landing on Earth, continuing the war from there; but reduced to small skirmishes out if and away from human attention. It kept that way until three years ago, around the same time that Superman made his debut, the Cons went quiet and had remained so until Megatron's return last week. While they doubted Megatron survived the Space Bridge explosion, the Cons were no less dangerous; especially since Starscream has no doubt taken command.

Superman and J'onn understood how the Autobots felt; losing your home world was heartbreaking.

Diana and Hawkgirl understood war all too well; the former had been trained since birth while the latter's people was embroiled in one now; Hawkgirl was glad her race wasn't going to try and conquer this world, she'd dread what it would be like to have the Autobots as enemies

Lantern felt a little guilty about not trusting them earlier but made a note to ask the Guardians about Cybertron.

Batman was suspicious a bit, however, he sympathized with their plight of losing nearly everything.

Flash remained silent, not giving away what he was thinking but was the next to speak.

"So what happens now, do you guys go back to hiding?"

"Everyone across the planet would have seen us now, no sense in that," Ratchet answered; the other Autobots looked to each other in confusion.

"If I may, I have something to say," all eyes turned to the speaker: Superman.

"I once thought I could protect the world by myself but I was wrong. Working together we saved the planet and I believe that if we stay together as a team we could become a force that fights for the ideals of peace and justice." He said seriously to them.

"What, like a bunch of super friends?" asked the Flash getting the idea he was talking about.

"More like a justice league." he said with a smile and placed his hand out.

"Do you have any idea how corny that sounds?" voiced the Flash again in humor.

"But maybe the big man's got a point, with all of us behind it, it might just work, count me in." he reassured putting his hand on Superman's.

"Me too" said Green Lantern approaching them and putting his hand over Flash's.

Hawkgirl followed his example "and me" placing her hand on his.

"My mother may not approve, but I find man's world to be intriguing, I'll gladly join." She said with confidence placing her hand on Hawkgirl's.

"What about you guys?" Flash asked the Bots.

"It would make things easier if we could do missions without worrying about stealth," Bulkhead noted.

"Plus, we could use the help against the Cons," Arcee added.

Bumblebee chirped in agreement while Ratchet remained silent. They all looked at Optimus for his decision.

"It would seem my compatriots believe that it would be a good idea… as I do as well."

"Looks like we're in," Arcee confirmed.

Then all turned towards the Dark Knight.

"What about you Batman?" The man of steel asked his counterpart.

"I'm not really a people person, but when you need help, and you will, call me."

"Understood" answered the man of steel, "Then we're all agreed?"

Diana looked around "Wait, J'onn is not here."

"Yeah, where'd he go?" asked the Flash.

They found J'onn sitting on the roof of the base, staring out at the horizon.

"J'onn, are you all right?" asked Superman.

"My family and loved ones are long gone; I am the last of my kind." He said with an aching heart.

Superman placed a hand on his shoulder, completely understanding where he was coming from.

"I know the feeling."

"Mars is dead, and I am alone in the Universe."

"J'onn, we can never replace the family you lost, but we'd be honored if you learn to call Earth home." Clark said in a warm tone.

J'onn thought it over then smiled and extended his hand towards him, and he replied in kind.

Through it all, Agent Fowler stayed in the back smiling.

"We're gonna be busy."

* * *

 **A/N: And so ends Secret Origins. I'd like to get this out there to avoid any confusion; there will be NO watchtower. I'm going this way for a couple of reasons: 1) The Justice League base inside a mountain is a call back to the team's first base in the comics: the Secret Sanctuary; the watchtower came later. 2) The Decepticons have a warship capable of interstellar travel so having an orbital satellite kind of paints a bullseye on them, especially since they're looking for the Autobot base.**

 **Next Episode: Scrapheap**


End file.
